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This Week in Nucleic Acids Research: Oct 28, 2015

University of Missouri researchers introduce a newly updated version of the Bovine Genome Database, a resource intended to improve genome annotation and data mining opportunities for those studying the Bos taurus genome. With such goals in mind, the team used the original B. taurus reference genome assembly, an alternative genome assembly, and RNA sequence data from dozens of bovine tissue types to come up with improved tools for browsing and annotating the genome. The site also makes it possible to integrate genome sequence, annotation, variants, gene expression, and quantitative trait loci through a tool dubbed BovineMine, which makes use of external gene function, pathway, orthology, and model organism information.

A team from Australia and Singapore presents an online resource for bringing together genomic and proteomic data on colorectal cancer samples and cell lines in a manner that makes it possible to directly compare the samples to one another. The integrated database, known as the Colorectal Cancer Atlas, contains information on tens of thousands of sequence variants detected in more than 13,700 colorectal cancer samples and 165 cell lines as well as proteomic profiles produced in quantitative or non-quantitative manner, the researchers explain. "The database enables the analysis of these data in the context of signaling pathways, protein-protein interactions, gene ontology terms, protein domains, and post-translational modifications," they add.

Danish researchers describe a database designed to encompass blood formation-related gene expression information that expands on data originally included in the HemaExplorer database. The site, dubbed BloodSpot, currently houses almost two dozen curated gene expression datasets generated for normal and malignant human and mouse hematopoietic cells that were sorted using FACS analysis. Within the larger database, the team put together set of 2,000 samples known as BloodPool that were originally produced through several past acute myeloid leukemia studies. "This new integrated data set provides the most detailed picture of the gene expression landscape in healthy and malignant hematopoiesis to date," the study's authors say, noting that BloodSpot "provides the possibility of comparing user-supplied leukemia samples to healthy cells."